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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcttgctcagatgaaattgcgtaccgtatattgtgtgctctttattaacctctgttgtgctcattccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGCAGAACCTGCGTTGTCTATGCTCCAGCGGAATGAGAACACCAAGAGGCAG

Basic information

species Oryza sativa
transcript LOC_Os02g32660.1
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32660.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G032628_T01 (Zea mays), 3'ss of exon 21
gtaagtcttgct-cagatgaaattgc-----gtac-cgtatattg-tgtgctctttat----------taacctctgttgtgctcattccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGCAGAACCTGCGTTGTCTATGCTCCAGCGGAATGAGAACACCAAGAGGCAG--
|||||| |||   ||  ||| | |||     |||| |  || |     || || | |           |||| |||||| ||  |||| ||||||||| ||||| ||||| || ||||| || || ||||| |||||| | || |||||||| || || ||||||||||||| ||| ||| | |     |     |  
gtaagttttgtggcacgtgatactgctctaggtacgcagatgtcaacttgttcctgacagaggtgaactaacttctgttatggccattacttgcagGACTGTTCGCATGATAATAGGCCATATTCATTCTCGGTTTATACACCAAGCAGAACATGTGTCGTCTATGCTCCAGTGGAGTGATAGCG--GGGTACTCGTT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88551368|gb|CI481420.1|CI481420
EST:     GGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: GGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|88331395|gb|CI675728.1|CI675728
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCCTCCTAG
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATT-CTCCTAG
EST: gi|55440790|gb|CV733707.1|CV733707
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|86436924|gb|CI118646.1|CI118646
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|88538824|gb|CI467885.1|CI467885
EST:     ACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: ACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|2797177|gb|AA750471.1|AA750471
EST:     CTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: CTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|87017784|gb|CI273806.1|CI273806
EST:     CACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGCCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: CACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|2797358|gb|AA750652.1|AA750652
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|86597068|gb|CI272663.1|CI272663
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|88412500|gb|CI688850.1|CI688850
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|88528801|gb|CI457067.1|CI457067
EST:     GGATTTGGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGGCCCTACTCGTTCTCAGTTTATTCTCCTAG
genomic: GGATTT-GGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACA-GGCCCTACTCGTTCTCAGTTTATTCTCCTAG
EST: gi|86478949|gb|CI121582.1|CI121582
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|2798141|gb|AA751435.1|AA751435
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|2799495|gb|AA752484.1|AA752484
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|86480418|gb|CI123051.1|CI123051
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|88851918|gb|CI679476.1|CI679476
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|88539730|gb|CI469711.1|CI469711
EST:     TGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|88535266|gb|CI464058.1|CI464058
EST:     ATCACACTGCAGAGCACTTCAGTGCC                         GATTGTTCACATAACAACAGGCCCTACTCGTTTTCAGTTTATTCTCCTAGC
genomic: ATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|88582727|gb|CI700155.1|CI700155
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|88538134|gb|CI467137.1|CI467137
EST:     TCTTTGGTGGATTGGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|86527618|gb|CI167824.1|CI167824
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|86526879|gb|CI167085.1|CI167085
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|86479150|gb|CI121783.1|CI121783
EST:     TCTTTAGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|2799484|gb|AA752473.1|AA752473
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGA
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGA
EST: gi|88432744|gb|CI690588.1|CI690588
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|88549688|gb|CI479595.1|CI479595
EST:     TGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|88529373|gb|CI457683.1|CI457683
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
EST: gi|88524423|gb|CI452333.1|CI452333
EST:     TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCC                         GATTGTTCACATGACNACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC
genomic: TCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 63 (upstream exon), 65 (downstream exon)
Score: 9

GTGGTCTTGGACTCAGATGCTGGACTCTTTGGTGGATTTGGCAGGATCCATCACACTGCAGAGCACTTCACTGCCgtaagtcttg ... ttccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGCAGAACCTGCGTTGTCTATGCTCCAGCGGAATGAGAACACCAAGAGGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcgtaccgtatattgtgtgctctttattaacctctgttgtgctcattccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGCAGAACCTGCGTTGTCTATGCTCCAGCGGAATGAGAACACCAAGAGGCAG
                        tattaac  putative branch site (score: 9)
                                         ctcattcctt  putative PPT
                    tctttattaa  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcttgctcagatgaaattgcgtaccgtatattgtgtgctctttattaacctctgttgtgctcattccttgcagGATTGTTCACATGACAACAGGCCCTACTCGTTCTCAGTTTATTCTCCTAGCAGAACCTGCGTTGTCTATGCTCCAGCGGAATGAGAACACCAAGAGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG